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While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
An adiabatic transition between two equilibrium states corresponding to different stiffnesses in an infinite chain of particles is studied. Initially, the chain particles have random displacements and random velocities corresponding to a…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that…
For classical systems, expectation value of macroscopic property in equilibrium state can be typically provided through thermodynamic (so-called canonical) average, where summation is taken over possible states in phase space (or in…
Thermodynamic formulas for investigating systems with density and/or temperature dependent particle masses are generally derived from the fundamental derivation equality of thermodynamics. Various problems in the previous treatments are…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
By classical and path-integral molecular dynamics simulations, we study the pressure-temperature ($P$-$T$) phase diagram of LaH$_{10}$ to clarify the impact of temperature and atomic zero-point motions. We calculate the XRD pattern and…
Gene expression data, or transcription data, are surrogates for actual protein concentrations in the cells. In addition protein-protein interactions are static diagrams of all the protein-protein interactions in the cell. These interactions…
The problem of the calculation of equilibrium thermodynamic properties and the establishment of statistical-thermodynamically-consistent finite bound-state partition functions in nonideal multi-component plasma systems is revised within the…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
The theoretical case is considered where the total amount of plasma protein is conserved, but the drug is eliminated after its single application. After a single drug application at time t = 0, the total drug concentration is measured at…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
Rigidity analysis using the "pebble game" has been applied to protein crystal structures to obtain information on protein folding, assembly and t he structure-function relationship. However, previous work using this technique has not made…
Chemical theories involving thermodynamical equilibrium states invariably utilize statistical mechanical equilibrium density distributions. Here, a definition of heat-work transformation termed thermo mechanical coherence is first made, and…